The present invention discloses a protein chip fully-automated high-throughput analysis apparatus, which comprises a control host machine, a display electrically connected to the control host machine, and a fully-automatic protein chip workstation, wherein the table surface of the fully-automatic protein chip workstation is provided with a sample treatment, a reagent treatment system, a plate washing system and a signal acquisition system, a free mechanical arm and a liquid adding system are added above the table surface of the work station, and the sample treatment system comprises a suction head support frame, a sample support frame, a reagent support frame and a barcode scanner. With the protein chip analysis apparatus of the present invention, the simultaneous detection on the multiple samples, the standard substance and the quality control substance can be achieved, the calculation on the concentration of the current batch of the samples through the current batch of the standard substance and the quality control substance is achieved, and the detection result is accurate and stable; and the multiple samples share the one standard substance or quality control substance so as to achieve the agent saving effect.